msDat {PepSAVIms}

Constructor for class msDat

Description

Creates a data structure encapsulating the mass spectrometry intensity readings as well as identifying information

Usage

msDat(mass_spec, mtoz, charge, ms_inten = NULL)

Arguments

mass_spec

Either a matrix or data.frame. This object must contain mass spectrometry abundances, and may optionally contain mass-to-charge values, charge state information, or additional extraneous variables. The mass spectrometry data is expected to be in a form with each column corresponding to a variable and each row corresponding to a mass-to-charge level.

For example, suppose that a collection of mass spectrometry intensity observations has provided data for 50 fractions across 20,000 mass-to-charge values. Then the input for mass_spec should be a matrix or data.frame with 20,000 rows and 50 or more columns. The additional columns beyond the 50 containing the mass spectrometry intensities can be the mass-to-charge data, the charge data, or other extraneous variables (the extraneous variables will be discarded when constructing the msDat object).

mtoz

A vector of either length 1 or length equal to the number of mass-to-charge values for which mass spectrometry data was collected, and which helps identify the mass-to-charge values for this data in one of several ways.

One way to provide the information is to provide a numeric vector where each entry provides the mass-to-charge value for a corresponding row of mass spectrometry data. Then the k-th entry of the vector would provide the mass-to-charge value for the k-th row of the mass spectrometry data.

A second way is to provide a single number which specifies the column index in the matrix or data.frame provided as the argument for the mass_spec parameter, such that this column contains the mass-to-charge information.

A third way is provide a single character string which provides the column name in the matrix or data.frame provided as the argument for the mass_spec parameter, such that this column contains the mass-to-charge information. Partial matching is supported.

charge

The information for the charge parameter can be provided in the same manner as for the mass-to-charge values.

ms_inten

Either NULL or a vector either of mode character or mode numeric specifying which of the variables in the argument to mass_spec are to be retained as the mass spectrometry intensity data. If NULL, then it is taken to mean that the entirety of the data in mass_spec, after removing variables in the data that are specified as arguments, is the mass spectrometry intensity data. If it is a numeric vector, then the entries should provide the indices for the region of interest in the mass spectrometry data in the argument for msObj. If it is a character vector, then the entries should uniquely specify the region of interest through partial string matching.

Details

Since the mass spectrometry data could conceivably be available to the researcher in a variety forms, this function attempts to provide a uniform data structure for encapsulating this information. It is the fundamental data structure containing the mass spectrometry data used internally by the filterMS and rankEN routines. The external interface for msDat is provided to the user so that specifying the mass spectrometry information can be made in a distinct step from performing statistical analyses, which it is hoped makes interfaces for the downstream analysis routines simpler and more intuitive to use.

Value

Returns an object of class msDat. This class is a list with elements described below. The class is equipped with a print and extractMS function.

ms

A matrix containing mass spectrometry intensity readings. Each column provides the mass spectrometry values for a given fraction, and each row provides the mass spectrometry values for a given mass-to-charge ratio value across the fractions.

mtoz

A vector with length equal to the number of mass-to-charge values provided in the mass spectrometry data, such that the k-th entry in the vector provides the mass-to-charge value for the k-th row of mass spectrometry data

chg

A vector with length equal to the number of mass-to-charge values provided in the mass spectrometry data, such that the k-th entry in the vector provides the charge information for the k-th row of mass spectrometry data

Examples

# Load mass spectrometry data
data(mass_spec)

# Convert mass_spec from a data.frame to an msDat object
ms <- msDat(mass_spec = mass_spec,
            mtoz = "m/z",
            charge = "Charge",
            ms_inten = c(paste0("_", 11:43), "_47"))

# Dimension of the data
dim(ms)

# Print the first few rows and columns
ms[1:5, 1:2]

# Let's change the fraction names to something more concise
colnames(ms) <- c(paste0("frac", 11:43), "frac47")

# Print the first few rows and columns with the new fraction names
ms[1:5, 1:8]

# Suppose there are some m/z levels that we wish to remove
ms <- ms[-c(2, 4), ]
# Print the first few rows and columns after removing rows 2 and 4
ms[1:5, 1:8]

# Suppose that there was an instrumentation error and that we need to change
# some values
ms[1, paste0("frac", 12:17)] <- c(55, 57, 62, 66, 71, 79)
# Print the first few rows and columns after changing some of the values in
# the first row
ms[1:5, 1:10]